imputationtool.ImputationTool Maven / Gradle / Ivy
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package imputationtool;
import imputationtool.postprocessing.BeagleImputationQuality;
import imputationtool.postprocessing.TriTyperDatasetCorrelator;
import imputationtool.postprocessing.TriTypertoPedMapDatExcludedSNPAnalyzer;
import imputationtool.preprocessing.BatchGenerator;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.regex.Pattern;
import umcg.genetica.io.trityper.converters.BeagleImputedToTriTyper;
import umcg.genetica.io.trityper.converters.FinalReportToTriTyper;
import umcg.genetica.io.trityper.converters.ImputeImputedToTriTyperV2;
import umcg.genetica.io.trityper.converters.MachImputedToTriTyper;
import umcg.genetica.io.trityper.converters.MinimacImputedToTriTyper;
import umcg.genetica.io.trityper.converters.PedAndMapToTriTyper;
import umcg.genetica.io.trityper.converters.TriTyperReferenceConcordantPedAndMapExporter;
import umcg.genetica.io.trityper.converters.TriTyperToPedAndMapConverter;
import umcg.genetica.io.trityper.converters.TriTyperToPlinkDosage;
import umcg.genetica.io.trityper.converters.TriTyperToVCF;
import umcg.genetica.io.trityper.converters.VCFToTriTyper;
import umcg.genetica.io.trityper.util.TriTyperConcatDatasets;
import umcg.genetica.io.trityper.util.TriTyperGenotypeDataMerger;
/**
*
* @author harm-jan
*/
public class ImputationTool {
public static final Pattern SEMI_COLON_PATTERN = Pattern.compile(";");
public static final String VERSION = ImputationTool.class.getPackage().getImplementationVersion();
public static void main(String[] args) {
System.out.println("ImputationTool " + VERSION + "\n\n");
try {
ImputationTool t = new ImputationTool();
if (args.length == 0) {
t.printUsage();
} else {
t.processArgs(args);
}
} catch (IOException e) {
e.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
}
System.exit(0);
}
private void processArgs(String[] args) throws IOException, Exception {
String mode = null;
String out = null;
String in = null;
String inName = null;
String in2 = null;
String in2Name = null;
String fam = null;
String hap = null;
String tmp = null; // template
String ext = null; // extension
Integer chr = null; // chromosome
Integer size = null; // sample size
String batch = null; // batch file
String beagle = null;
String batchdesc = null; // batch description
String snps = null; // snp list
Double threshold = null; // correlation threshold
String exclude = null;
Integer chrStart = 1;
Integer chrEnd = 22;
Integer nrSamples = null;
String sampleFile = null;
String sampleFileToInclude = null;
String pattern = null;
String fileMatchRegex = null;
boolean splitbychromosome = false;
for (int i = 0; i < args.length; i++) {
String arg = args[i];
String val = null;
if (i + 1 < args.length) {
val = args[i + 1];
}
if (arg.equals("--mode")) {
mode = val;
} else if (arg.equals("--out")) {
out = val;
} else if (arg.equals("--in")) {
in = val;
} else if (arg.equals("--name")) {
inName = val;
} else if (arg.equals("--pattern")) {
pattern = val;
} else if (arg.equals("--in2")) {
in2 = val;
} else if (arg.equals("--name2")) {
in2Name = val;
} else if (arg.equals("--hap")) {
hap = val;
} else if (arg.equals("--fam")) {
fam = val;
} else if (arg.equals("--tpl")) {
tmp = val;
} else if (arg.equals("--chr")) {
try {
chr = Integer.parseInt(val);
} catch (NumberFormatException e) {
System.out.println("Value supplied for --chr is not an integer");
System.exit(-1);
}
chrStart = chr;
chrEnd = chr;
} else if (arg.equals("--batch-file")) {
batch = val;
} else if (arg.equals("--size")) {
try {
size = Integer.parseInt(val);
} catch (NumberFormatException e) {
System.out.println("Value supplied for --size is not an integer");
System.exit(-1);
}
} else if (arg.equals("--exclude")) {
exclude = val;
} else if (arg.equals("--beagle")) {
beagle = val;
} else if (arg.equals("--batchdesc")) {
batchdesc = val;
} else if (arg.equals("--snps")) {
snps = val;
} else if (arg.equals("--split")) {
splitbychromosome = true;
} else if (arg.equals("--chrstart")) {
try {
chrStart = Integer.parseInt(val);
} catch (NumberFormatException e) {
System.out.println("Value supplied for --chrStart is not an integer");
System.exit(-1);
}
} else if (arg.equals("--chrend")) {
try {
chrEnd = Integer.parseInt(val);
} catch (NumberFormatException e) {
System.out.println("Value supplied for --chrEnd is not an integer");
System.exit(-1);
}
} else if (arg.equals("--threshold")) {
try {
threshold = Double.parseDouble(val);
} catch (NumberFormatException e) {
System.out.println("Value supplied for --threshold is not an double");
System.exit(-1);
}
} else if (arg.equals("--nrSamples")) {
try {
nrSamples = Integer.valueOf(val);
} catch (NumberFormatException e) {
System.out.println("Value supplied for --nrSamples is not an integer");
System.exit(-1);
}
} else if (arg.equals("--samples")) {
sampleFile = val;
} else if (arg.equals("--samplestoinclude")) {
sampleFileToInclude = val;
} else if (arg.equals("--fileMatchRegex")) {
fileMatchRegex = val;
}
}
if (mode == null) {
System.out.println("Mode is null");
printUsage();
} else if (mode.equals("btt")) {
convertImputedBeagleToTriTyper(in, tmp, ext, out, fam);
// --mode btt --in indir --tpl template --ext ext --out outdir --fam famfile
} else if (mode.equals("bttb")) {
System.out.println("in:\t" + in);
System.out.println("tpl:\t" + tmp);
System.out.println("size:\t" + size);
System.out.println("out:\t" + out);
convertImputedBeagleToTriTyperFromBatches(in, tmp, out, size, chrStart, chrEnd);
// --mode bttb --in indir --tpl template --out outdir --size samplesize
} else if (mode.equals("ttpd")) {
convertTriTyperToPlinkDosage(in, out, fam, splitbychromosome);
// --mode ttpd --in indir --beagle beagledir --tpl template --batchdescriptor batchdescriptor --out outdir --fam famfile
} else if (mode.equals("ttpm")) {
convertTriTyperToPedAndMap(in, out, fam, snps, splitbychromosome, sampleFile);
// --mode ttpm --in indir --out outdir --fam famfile
} else if (mode.equals("ftt")) {
convertFinalReportToTriTyper(in, out);
// --mode ttpm --in indir --out outdir --fam famfile
} else if (mode.equals("ttpmh")) {
convertTriTyperToPedAndMapHapMap(in, hap, out, fam, batch, chr, exclude, false);
// --mode ttpmh --in indir --hap hapmapdir --out outdir --fam famfile --batch-file batchfile --chr chromosome
} else if (mode.equals("corr")) {
System.out.println("in:\t" + in);
System.out.println("inname:\t" + inName);
System.out.println("in2:\t" + in2);
System.out.println("in2name:\t" + in2Name);
System.out.println("out:\t" + out);
correlateDatasets(in, inName, in2, in2Name, out, snps);
// --mode corr --in indir --inname name --in2 indir2 --in2name inname2 --out outdir --snps snplist
} else if (mode.equals("pmtt")) {
convertPedAndMapToTriTyper(in, out);
// --mode pmtt --in indir --out outdir
} else if (mode.equals("ecra")) {
getExcludedSNPsWithCallRate(in, threshold);
// --mode ecra --in indir --threshold threshold
} else if (mode.equals("r2dist")) {
createR2Distributions(in, tmp, out, size);
// --mode r2dist --in indir --tpl template --out outdir --size numbatches
} else if (mode.equals("batch")) {
createBatches(in, out, size);
// --mode batch --in indir --tpl template --out outdir --size batchsize
} else if (mode.equals("corrb")) {
System.out.println("in:\t" + in);
System.out.println("inname:\t" + inName);
System.out.println("in2:\t" + in2);
System.out.println("in2name:\t" + in2Name);
System.out.println("out:\t" + out);
correlateDatasets(in, inName, in2, in2Name, out, snps, beagle, tmp, size);
} else if (mode.equals("merge")) {
System.out.println("in");
System.out.println("in2");
System.out.println("out");
concatDatasets(in, in2, out, snps);
} else if (mode.equals("concat")) {
System.out.println("in:\t" + in);
System.out.println("out:\t" + out);
concatDatasets(in, out);
} else if (mode.equals("itt")) {
System.out.println("in:\t" + in);
System.out.println("out:\t" + out);
System.out.println("nrSamples:\t" + nrSamples);
convertImputeToTriTyper(in, out, nrSamples, sampleFile, sampleFileToInclude, fileMatchRegex, snps);
} else if (mode.equals("ttvcf")) {
System.out.println("in:\t" + in);
System.out.println("out:\t" + out);
convertTriTyperToVcf(in, out);
} else if (mode.equals("vcftt")) {
System.out.println("in:\t" + in);
System.out.println("out:\t" + out);
System.out.println("pattern:\t" + pattern);
convertVCFToTriTyper(in, out, pattern);
} else if (mode.equals("mmtt")) {
System.out.println("in:\t" + in);
System.out.println("out:\t" + out);
convertMinimacToTriTryper(in, out);
} else if (mode.equals("mtt")) {
System.out.println("in:\t" + in);
System.out.println("out:\t" + out);
convertMachToTriTyper(in, out);
} else if (mode.equals("mmtt2")) {
System.out.println("in:\t" + in);
System.out.println("out:\t" + out);
convertMinimacToTriTryper2(in, out);
} else {
printUsage();
}
// else if (mode.equals("pmbg")) {
// System.out.println("in:\t" + in);
// System.out.println("batch:\t" + batch);
// convertPedAndMapToBeagle(in, batch);
// }
}
public void printUsage() {
System.out.println("------------------------\nPreProcessing\n------------------------\n");
System.out.println("# Create random batches of cases and controls from a TriTyper dataset. Creates a file called batches.txt in outdir.\n"
+ "--mode batch --in TriTyperdir --out outdir --size batchsize\n");
System.out.println("------------------------\nIllumina FinalReport files\n------------------------\n");
System.out.println("# Convert a dir with MACH imputed data into TriTyper\n"
+ "--mode ftt --in finalreportfile --out TriTyperDir");
System.out.println("------------------------\nImputation\n------------------------\n");
System.out.println("# Convert Impute Imputed data into TriTyper\n"
+ "--mode itt --in ImputeDir --out TriTyperDir --nrSamples numberOfSamplesInImputedData [--samples samplelistfile.txt] [--samplestoinclude samplelistfiletoinclude.txt] [--fileMatchRegex pattern] [--snps snpfile.txt]");
System.out.println("# Convert a dir with MACH imputed data into TriTyper\n"
+ "--mode mtt --in Imputation restult dir --out TriTyperDir");
System.out.println("# Convert a dir with Minimac imputed data into TriTyper\n"
+ "--mode mmtt --in Imputation restult dir --out TriTyperDir");
System.out.println("# Convert a single Minimac imputed file into TriTyper\n"
+ "--mode mmtt2 --in Imputation restult file prefix (.info and .dose should be present) --out TriTyperDir");
System.out.println();
System.out.println("------------------------\nBeagle\n------------------------\n");
System.out.println("# Convert beagle files (one file/chromosome) to TriTyper. Filetemplate is a template for the batch filenames, The text CHROMOSOME will be replaced by the chromosome number.\n"
+ "--mode btt --in BeagleDir --tpl template --ext ext --out TriTyperDir [--fam famfile]\n");
System.out.println("# Convert batches of beagle files (multiple files / chromosome) to trityper files. Filetemplate is a template for the batch filenames, The text CHROMOSOME will be replaced by the chromosome number, BATCH by the batchname.\n"
+ "--mode bttb --in BeagleDirdir --tpl template --out TriTyperDir --size numbatches [--chr chromosome] [--chrstart startchr] [--chrend endchr]\n");
System.out.println("------------------------\nPed+Map (Plink files)\n------------------------\n");
System.out.println("# Converts Ped and Map files created by ttpmh to Beagle format\n"
+ "--mode pmbg --in indir --batch-file batches.txt\n");
System.out.println("# Converts TriTyper file to Plink Dosage format. Filetemplate is a template for the batch filenames, The text CHROMOSOME will be replaced by the chromosome number, BATCH by the batchname.\n"
+ "--mode ttpd --in indir --out outdir --fam famfile [--split]\n");
System.out.println("# Converts PED and MAP files to TriTyper.\n"
+ "--mode pmtt --in Ped+MapDir --out TriTyperDir\n");
System.out.println("# Converts TriTyper file to PED and MAP files. The FAM file is optional. --split splits the ped and map files per chromosome. Providing a SNP file will override --split\n"
+ "--mode ttpm --in indir --out outdir [--fam famfile] [--split] [--snps snpfile]\n");
System.out.println("# Converts TriTyper dataset to Ped+Map concordant to reference (hap) dataset. Supply a batchfile if you want to export in batches. Supply a chromosome if you want to export a certain chromosome.\n"
+ "--mode ttpmh --in TriTyperDir --hap TriTyperReferenceDir --out outdir [--fam famfile] [--batch-file batchfile] [--chr chromosome] [--exclude fileName]\n");
System.out.println("---------------------\nPostProcessing\n---------------------\n");
System.out.println("# Correlates genotypes of imputed vs non-imputed datasets. Saves a file called correlationOutput.txt in outdir, containing correlation per chromosome as well as correlation distribution.\n"
+ "--mode corr --in TriTyperDir --name datasetname --in2 TriTyperDir2 --name2 datasetname2 --out outdir [--snps snplist]\n");
System.out.println("# Correlates genotypes of imputed vs non-imputed datasets. Also take Beagle imputation score (R2) into account. Saves a file called correlationOutput.txt in outdir, containing correlation per chromosome as well as correlation distribution.\n"
+ "--mode corrb --in TriTyperDir --name datasetname --in2 TriTyperDir2 --name2 datasetname2 --out outdir --beagle beagleDir --tpl template --size numBatches \n");
System.out.println("# Gets all the excluded snps from chrx.excludedsnps.txt with a certain call-rate threshold (0 < threshold < 1.0)\n"
+ "--mode ecra --in TriTyperDir --threshold threshold\n");
System.out.println("# Generates R2 distribution (beagle quality score) for each batch and chromosome, and tests each batch against chromosome R2 distribution, using WilcoxonMannWhitney test\n"
+ "--mode r2dist --in BeagleDir --template template --out outdir --size numbatches\n");
System.out.println("# Merge two TriTyper datasets\n"
+ "--mode merge --in TriTyper1Dir --in2 TryTyper2Dir --out outdir\n");
System.out.println("# Concatinate TriTyper datasets. All should contain same number of individuals in the same order.\n"
+ "--mode concat --in \"TriTyperDir1;TriTyperDir2;TriTyperDirN\" --out outdir\n");
System.out.println("---------------------\nVCF\n---------------------\n");
System.out.println("# Convert TriTyper to VCF and vice versa\n"
+ "--mode ttvcf --in indir --out outdir \n"
+ "--mode vcftt --in indir --out outdir [--pattern pattern]\n");
System.exit(0);
}
private void convertTriTyperToPedAndMapHapMap(String baseDir, String hapmapDir, String outputDir, String famfile, String batchFile, Integer chromosome, String excludesnps, boolean singlefile) throws IOException {
if (baseDir == null || hapmapDir == null || outputDir == null) {
System.out.println("Please supply values for TriTyper inputdir (--in), HapMap dir (--hap) and outputdir (--out) when to running --mode ttpmh\n\n");
// printUsage();
System.exit(0);
}
TriTyperReferenceConcordantPedAndMapExporter ttb = new TriTyperReferenceConcordantPedAndMapExporter();
ttb.export(hapmapDir, baseDir, batchFile, excludesnps, outputDir);
}
private void convertTriTyperToPedAndMap(String baseDir, String outputDir, String famfile, String snpList, boolean splitbychromosome, String samplesToInclude) throws IOException, Exception {
if (baseDir == null || outputDir == null) {
System.out.println("Please supply values for TriTyper inputdir (--in) and outputdir (--out) when to running --mode ttpm\n\n");
// printUsage();
System.exit(0);
}
TriTyperToPedAndMapConverter ttpm = new TriTyperToPedAndMapConverter();
if (snpList != null) {
ttpm.exportSubsetOfSNPs(baseDir, outputDir, snpList, samplesToInclude);
} else {
ttpm.exportAllSNPs(baseDir, outputDir, splitbychromosome);
}
}
private void convertImputedBeagleToTriTyper(String inputLocation, String descriptor, String extension, String trityperoutputdir, String famfile) throws IOException {
if (inputLocation == null || descriptor == null || extension == null || trityperoutputdir == null) {
System.out.println("Please supply values for Beagle inputdir (--beagle), file template (--tpl), batch descriptor (--batchdesc) and TriTyper outputdir (--out) when to running --mode btt\n\n");
// printUsage();
System.exit(0);
}
BeagleImputedToTriTyper btt = new BeagleImputedToTriTyper();
if (famfile != null) {
btt.loadFamFile(famfile);
}
btt.importImputedDataWithDosageInformationBeagle(inputLocation, descriptor, extension, trityperoutputdir);
}
private void convertImputedBeagleToTriTyperFromBatches(String inputLocation, String descriptor, String outputLocation, Integer numBatches, Integer chrStart, Integer chrEnd) throws IOException {
if (inputLocation == null || descriptor == null || outputLocation == null || numBatches == null) {
System.out.println("Please supply values for Beagle inputdir (--beagle), file template (--tpl), number of batches (--size) and TriTyper outputdir (--out) when to running --mode bttb\n\n");
System.exit(0);
// printUsage();
}
BeagleImputedToTriTyper btt = new BeagleImputedToTriTyper();
btt.importImputedDataWithDosageInformationBeagleBatches(inputLocation, descriptor, numBatches, outputLocation, chrStart, chrEnd);
}
private void correlateDatasets(String dataset1, String dataset1Name, String dataset2, String dataset2Name, String output, String snpList) throws IOException {
if (dataset1 == null || dataset1Name == null || dataset2 == null || dataset2Name == null || output == null) {
System.out.println("Please supply values for dataset location (--in), datasetname (--name), dataset 2 location (--in2), dataset 2 name (--name2), and output location (--out)\n\n");
System.exit(0);
}
TriTyperDatasetCorrelator c = new TriTyperDatasetCorrelator(dataset1, dataset1Name, dataset2, dataset2Name);
if (snpList != null) {
c.confineToSNPs(snpList);
}
c.run(output);
}
private void getExcludedSNPsWithCallRate(String location, Double threshold) throws IOException {
if (location == null || threshold == null) {
System.out.println("Please supply values for input location (--in) and threshold (--threshold)\n\n");
System.exit(0);
}
TriTypertoPedMapDatExcludedSNPAnalyzer q = new TriTypertoPedMapDatExcludedSNPAnalyzer();
q.printSNPsWithCallRateHigherThan(threshold, location);
}
private void convertPedAndMapToTriTyper(String dataLocation, String outputLocation) {
if (dataLocation == null || outputLocation == null) {
System.out.println("Please supply values for input location (--in) and output (--out)");
System.exit(0);
}
PedAndMapToTriTyper p = new PedAndMapToTriTyper();
try {
p.importPEDFile(dataLocation, outputLocation);
} catch (IOException e) {
e.printStackTrace();
}
}
// private void convertPedAndMapToTriTyper(String dataLocation, String outputLocation, String mapdelimiter, int chrcol, int chrpos, int snpcol, String peddelimiter) {
// PedAndMapToTriTyper p = new PedAndMapToTriTyper();
// String[] casesToInclude = {"2"};
// p.importPEDFile(dataLocation, mapdelimiter, chrcol, chrpos, snpcol, peddelimiter, outputLocation, casesToInclude);
// }
// ttpd trityperdir beagledir datasetdescriptor batchdescriptor outputdir
private void convertTriTyperToPlinkDosage(String trityperdir, String outputdir, String famFile, boolean splitperchr) throws IOException {
// if(trityperdir == null || beagledir == null || datasetdescriptor == null || batchdescriptor == null || outputdir == null){
if (trityperdir == null || outputdir == null) {
System.out.println("Please supply values for TriTyper input (--in), beagle dir (--beagle), dataset descriptor (--tpl), batch descriptor (--batchdesc), and output dir (--out)\n\n");
System.exit(0);
}
TriTyperToPlinkDosage p = new TriTyperToPlinkDosage();
p.outputDosageInformation(trityperdir, outputdir, famFile, splitperchr);
// String inputFile, String datasetDir, String datasetDescription, String batchname, String outputDir
// p.splitDosageInformationPerChromosome(outputdir, beagledir, datasetdescriptor, batchdescriptor, outputdir);
}
private void createR2Distributions(String inputLocation, String descriptor, String outputLocation, Integer numBatches) throws IOException {
if (inputLocation == null || descriptor == null || outputLocation == null || numBatches == null) {
System.out.println("Please supply values for Beagle input dir (--in), dataset template (--tpl), outputlocation (--out) and num batches (--size)\n\n");
System.exit(0);
}
BeagleImputationQuality b = new BeagleImputationQuality();
b.determineImputationQualityDistribution(inputLocation, descriptor, numBatches, outputLocation);
}
private void createBatches(String in, String out, Integer size) throws IOException {
if (in == null || out == null || size == null) {
System.out.println("Please supply values for TriTyper input directory (--in), output directory (--out) and requested batch size (--size)\n\n");
System.exit(0);
}
BatchGenerator b = new BatchGenerator();
b.generateBatchesFromTriTyper(in, out, size);
}
private void correlateDatasets(String dataset1, String dataset1Name, String dataset2, String dataset2Name, String output, String snpList, String beagle, String tmp, Integer size) throws IOException {
if (dataset1 == null || dataset1Name == null || dataset2 == null || dataset2Name == null || output == null) {
System.out.println("Please supply values for dataset location (--in), datasetname (--name), dataset 2 location (--in2), dataset 2 name (--name2), and output location (--out)\n\n");
System.exit(0);
}
TriTyperDatasetCorrelator c = new TriTyperDatasetCorrelator(dataset1, dataset1Name, dataset2, dataset2Name, beagle, tmp, size);
if (snpList != null) {
c.confineToSNPs(snpList);
}
c.run(output);
}
private void concatDatasets(String in, String in2, String out, String snps) throws IOException {
if (in != null && in2 != null && out != null) {
TriTyperGenotypeDataMerger merger = new TriTyperGenotypeDataMerger();
merger.combinePrioritizerDatasetsMergeCommonSNPs(in, in2, out, snps);
} else {
System.out.println("Please provide: --in, --in2 and --out for --mode merge");
System.exit(0);
}
}
private void convertImputeToTriTyper(String in, String out, Integer nrSamples, String samplesFile, String samplesToIncludeFile, String fileMatchRegex, String snps) throws IOException, Exception {
if (in == null || out == null || nrSamples == null) {
System.out.println("Please provide: --in, --nrSamples and --out for --mode itt");
System.exit(0);
} else {
ImputeImputedToTriTyperV2 t = new ImputeImputedToTriTyperV2();
t.importImputedDataWithProbabilityInformationImpute(in, out, nrSamples, samplesFile, samplesToIncludeFile, fileMatchRegex, snps);
}
}
private void convertTriTyperToVcf(String in, String out) throws IOException, Exception {
if (in == null || out == null) {
System.out.println("Please provide: --in and --out for --mode ttvcf");
System.exit(0);
} else {
System.out.println("Warning! All genotypes are exported as if phased");
TriTyperToVCF ttvcfConvertor = new TriTyperToVCF();
ttvcfConvertor.convert(in, out, null);
}
}
private void convertVCFToTriTyper(String in, String out, String pattern) throws IOException, Exception {
if (in == null || out == null) {
System.out.println("Please provide: --in and --out for --mode vcftt");
System.exit(0);
} else {
VCFToTriTyper tt = new VCFToTriTyper();
tt.parse(in, out, pattern);
}
}
private void convertFinalReportToTriTyper(String in, String out) throws IOException {
boolean isIlluminaFinalReportFile = true;
String delimiter = "\t";
String decimalSeparator = ".";
// for (int a=0; a© 2015 - 2025 Weber Informatics LLC | Privacy Policy